biology/gffread: GFF/GTF format conversions, filtering, etc

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.  The program gffread can be used to validate,
filter, convert and perform various other operations on GFF files.
Because the program shares the same GFF parser code with Cufflinks,
Stringtie, and gffcompare, it could be used to verify that a GFF file
from a certain annotation source is correctly "understood" by these
programs.

5 files changed, 110 insertions, 0 deletions

diff --git a/biology/gffread/DESCR b/biology/gffread/DESCR
new file mode 100644
index 00000000000..2971ed7cbfa
--- /dev/null
+++ b/biology/gffread/DESCR
@@ -0,0 +1,7 @@
+GFF/GTF utility providing format conversions, filtering, FASTA sequence
+extraction and more.  The program gffread can be used to validate,
+filter, convert and perform various other operations on GFF files.
+Because the program shares the same GFF parser code with Cufflinks,
+Stringtie, and gffcompare, it could be used to verify that a GFF file
+from a certain annotation source is correctly "understood" by these
+programs.
diff --git a/biology/gffread/Makefile b/biology/gffread/Makefile
new file mode 100644
index 00000000000..d3d40e9e0e0
--- /dev/null
+++ b/biology/gffread/Makefile
@@ -0,0 +1,19 @@
+# $NetBSD: Makefile,v 1.1 2022/11/06 23:01:17 bacon Exp $
+
+DISTNAME=	gffread-0.12.7
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=gpertea/}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon@NetBSD.org
+HOMEPAGE=	https://ccb.jhu.edu/software/stringtie/gff.shtml
+COMMENT=	GFF/GTF format conversions, filtering, FASTA extraction, etc
+LICENSE=	mit
+
+GITHUB_SUBMODULES=	gpertea gclib v0.12.7 gclib
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+INSTALL_TARGET=	install-strip
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/gffread/PLIST b/biology/gffread/PLIST
new file mode 100644
index 00000000000..b7c8618e2e6
--- /dev/null
+++ b/biology/gffread/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2022/11/06 23:01:17 bacon Exp $
+bin/gffread
diff --git a/biology/gffread/distinfo b/biology/gffread/distinfo
new file mode 100644
index 00000000000..f93aaa9acb6
--- /dev/null
+++ b/biology/gffread/distinfo
@@ -0,0 +1,9 @@
+$NetBSD: distinfo,v 1.1 2022/11/06 23:01:18 bacon Exp $
+
+BLAKE2s (gffread-0.12.7.tar.gz) = 4f39c075ca17fe6813595dd7c8d1ff2ff829f76b3d5eed46e28c7cbdaca56255
+SHA512 (gffread-0.12.7.tar.gz) = 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b
+Size (gffread-0.12.7.tar.gz) = 403734 bytes
+BLAKE2s (gpertea-gclib-v0.12.7.tar.gz) = 68a41720355aac7d8b0602a66c558cfdabd93594a9079761ab5332f7adece277
+SHA512 (gpertea-gclib-v0.12.7.tar.gz) = 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90
+Size (gpertea-gclib-v0.12.7.tar.gz) = 259314 bytes
+SHA1 (patch-Makefile) = 07e83c4b17715f31f0429671dba703a8b1d31118
diff --git a/biology/gffread/patches/patch-Makefile b/biology/gffread/patches/patch-Makefile
new file mode 100644
index 00000000000..89414e64340
--- /dev/null
+++ b/biology/gffread/patches/patch-Makefile
@@ -0,0 +1,73 @@
+$NetBSD: patch-Makefile,v 1.1 2022/11/06 23:01:18 bacon Exp $
+
+# Portability and package-friendliness
+
+--- Makefile.orig	2021-07-23 14:21:36.000000000 +0000
++++ Makefile
+@@ -1,11 +1,11 @@
+-GCLDIR := $(if $(GCLDIR),$(GCLDIR),../gclib)
++GCLDIR := $(if $(GCLDIR),$(GCLDIR),gclib)
+ 
+ SEARCHDIRS := -I. -I${GCLDIR}
+ 
+ SYSTYPE :=     $(shell uname)
+ 
+ CXX   := $(if $(CXX),$(CXX),g++)
+-LINKER  := $(if $(LINKER),$(LINKER),g++)
++LINKER  := $(if $(LINKER),$(LINKER),${CXX})
+ 
+ LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)
+ 
+@@ -15,7 +15,7 @@ BASEFLAGS  := -Wall -Wextra -std=c++11 $
+ 
+ GCCV8 := $(shell expr `${CXX} -dumpversion | cut -f1 -d.` \>= 8)
+ ifeq "$(GCCV8)" "1"
+- BASEFLAGS += -Wno-class-memaccess
++ # BASEFLAGS += -Wno-class-memaccess
+ endif
+ 
+ CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))
+@@ -33,7 +33,7 @@ else #debug builds
+     LDFLAGS += -pg
+   else
+     #CXXFLAGS += -g -O0 -DNDEBUG
+-    CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
++    #CXXFLAGS += -g -O0 -DDEBUG -D_DEBUG -DGDEBUG
+   endif
+   ifneq (,$(filter %memcheck %memdebug, $(MAKECMDGOALS)))
+      #use sanitizer in gcc 4.9+
+@@ -79,10 +79,7 @@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArg
+  
+ .PHONY : all
+ 
+-all static release debug memcheck memdebug profile gprof prof: ../gclib gffread
+-
+-../gclib:
+-	git clone https://github.com/gpertea/gclib.git ../gclib
++all static release debug memcheck memdebug profile gprof prof: ${GCLDIR} gffread
+ 
+ $(OBJS) : $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+ gffread.o : gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h
+@@ -97,9 +94,21 @@ gffread: $(OBJS) gffread.o
+ 
+ # target for removing all object files
+ 
+-.PHONY : clean
++.PHONY : clean install install-strip
++
+ clean:
+ 	@${RM} gffread gffread.o* gffread.exe $(OBJS)
+ 	@${RM} core.*
+ 
++MKDIR	?= mkdir
++INSTALL	?= install
++STRIP	?= strip
++PREFIX	?= /usr/local
++DESTDIR	?= .
++
++install:
++	${MKDIR} -p ${DESTDIR}${PREFIX}/bin
++	${INSTALL} -c gffread ${DESTDIR}${PREFIX}/bin
+ 
++install-strip: install
++	${STRIP} ${DESTDIR}${PREFIX}/bin/gffread